heatmapSpp: Visualise a distance matrix using a heatmap

In spider: Species Identity and Evolution in R

Description

This function plots a heatmap of the distance matrix, with shorter distances indicated by darker colours.

Usage

heatmapSpp(distObj, sppVector, col = NULL, axisLabels = NULL, triangle = "both", 
	showData = FALSE, dataRound = 3, dataCEX = 1)

Arguments

distObj	A matrix or object of class dist.
sppVector	The species vector. See sppVector.
col	A vector giving the colours for the heatmap.
axisLabels	A character vector that provides the axis labels for the heatmap. By default the species vector is used.
triangle	Which triangle of the heatmap should be plotted. Possible values of "both", "upper" and "lower". Default of "both".
showData	Logical. Should the data be shown on the heatmap? Default of FALSE.
dataRound	The number of significant figures the printed data will show. Default of 3.
dataCEX	Size of text for printed data. Default of 1.

Details

The default palette has been taken from the colorspace package.

Value

Plots a heatmap of the distance matrix. Darker colours indicate shorter distances, lighter colours indicate greater distances.

Author(s)

Samuel Brown <[e-mail]>

Examples

data(dolomedes)
doloDist <- dist.dna(dolomedes, model = "raw")
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)
heatmapSpp(doloDist, doloSpp)
heatmapSpp(doloDist, doloSpp, axisLabels = dimnames(dolomedes)[[1]])

data(anoteropsis)
anoDist <- dist.dna(anoteropsis, model = "raw")
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
    function(x) paste(x[1], x[2], sep="_"))
heatmapSpp(anoDist, anoSpp)
heatmapSpp(anoDist, anoSpp, showData = TRUE)
heatmapSpp(anoDist, anoSpp, showData = TRUE, dataRound = 1, dataCEX = 0.4)
heatmapSpp(anoDist, anoSpp, triangle = "upper")
heatmapSpp(anoDist, anoSpp, triangle = "lower")
heatmapSpp(anoDist, anoSpp, triangle = "lower", showData = TRUE, dataRound = 1, dataCEX = 0.4)

spider documentation built on May 2, 2019, 5:16 p.m.